[gmx-users] constraints bond length vari by 10%
mark.abraham at anu.edu.au
Thu Jun 17 00:01:04 CEST 2010
----- Original Message -----
From: Sebastian Waltz <sebastian.waltz at physik.uni-freiburg.de>
Date: Thursday, June 17, 2010 2:23
Subject: Re: [gmx-users] constraints bond length vari by 10%
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Hi Mark,
> what I have written in the .top you can see in my first
OK - but my suggestion was that it was put in the wrong *place* and I don't have enough information to say whether that's true.
> I actually don't know what to write what and in
> which .itp/.tpr file I have to add something and I also
> can't find something in the Internet. The documentation for
> the constraints is just bad.
I understand your frustration, but documentation can't anticipate the answer to every question or it would be infinitely long. That fact doesn't make it bad. What the documentation can do is provide general instruction. If my guess is correct, then the worked example of a .top file in Chapter 5 will help you understand where [constraints] needs to go. Specifically, page 109 will point out that
[ moleculetype ]
Section 5.5 has a worked example of how to use [settles] which are a kind of constraint, and work the same way.
Once you've worked through this information, if you still have a problem with the documention, then a constructive suggestion for improvement would be welcome :-)
> On Wed, 16 Jun 2010 09:05:20 +1000
> Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > ----- Original Message -----
> > From: Sebastian Waltz
> > <sebastian.waltz at physik.uni-freiburg.de>
> > Date: Tuesday, June 15, 2010 22:09
> > Subject: [gmx-users] constraints bond length vari by 10%
> > To: gmx-users at gromacs.org
> > > Hi all,
> > >
> > > I added constraints on some bonds in my system by
> > adding
> > >
> > > [ constraints ]
> > > ;ai aj type distance
> > > 40 41 1 0.1230
> > > 47 48 1 0.1230
> > > 54 55 1 0.1230
> > > 61 62 1 0.1230
> > >
> > > to me top file (CO double bonds) and in the mdp file
> > >
> > > constraints
> > > = none
> > >
> > > . I thought this should more or less fix my bond
> > lengths.
> > > Nether the less the bond lengths vary by 10%. Did I
> > make
> > > something or is it quite normal? What would be the way
> > to
> > > fix the bond length so that they vary only by ca. 1%.
> > You're using the right approach, but you've probably not
> > put your [constraints] directive in the right
> > [moleculetype], or used the wrong .top/.itp/.tpr file at
> > some point.
> > Mark
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